Lesson 1 Exercise 9..extracting specific sequence "AACCGGUU"

[GitTodojetaime]

I am on lesson exercise 9 of the beginners seqkit tutorial. I am using this to extract sequences from hairpin.fa

seqkit grep -f ids.text hairpins.fa

5 patterns become loaded from the file with this command. What changes can I make to extract sequences with "AACCGGUU" specifically?

[robertaboukhalil]

Yes using seqkit grep -f can work here but you need to make sure the file ids.text only contains the sequences you're interested in (i.e. only AACCGGUU).

Also, note that seqkit grep by default matches patterns in the sequence name, not the sequence itself. Check out the manual for which flag you need to add in order to search for the pattern by sequence.

[GitTodojetaime]

On another note...I am trying to Use [seqkit seq] to create the file formatted.fa, which formats hairpins.fa to show 80 bases per line instead of the current 60 bases per line.I am using this code..

seqkit seq --max-len 80 hairpins.fa

It is generating an output that looks correct...sequences roughly 80 bp...but the tutorial I'm using isn't marking it as correct. I would love to know your thoughts.

[GitTodojetaime]

Thank you. :)

So I used the manual and found Region R- and I need to include the nucleotides as a "1 based index"...where A is 1, T is 2, G is 3, C is 4...but what about U? I notice there is an 'N" in the index..and I'm assuming this might stand for Uracil.

[GitTodojetaime]

Now I'm seeing -s might be for sequence..still not sure how to specify the sequence..

[robertaboukhalil]

seqkit seq --max-len 80 hairpins.fa would only show you sequences that have length 80, which is not what we need. We need sequences of all length, but only showing 80 nucleotides per line, which the --line-width does

Yes, you can use -s for sequence and then use --pattern to specifying the sequence pattern to search for

Also, just in case it's not clear in the UI, you need to redirect the output of the tool to the file specified in the exercise.

[GitTodojetaime]

Thank you for the clarification..I misread the challenge :) The file is called formatted.fa which I have already created..
This is the command I tried seqkit seq --line-width 80 formatted.fa
Not...working
Any recommendations on redirecting the file?

[robertaboukhalil]

On the command line, you need to use command > output.txt to redirect the output of command to output.txt, i.e. seqkit seq -w 80 hairpins.fa > formatted.fa